Yeah, I'm running into this not only individual pages, but an entire site. I have a lot of customized code spread across multiple pages, and if I ever want to change templates, I'll need to change that code. Since it's a heavily trafficked site, it'll be a nightmare. Right now I'm banking on the fact that Squarespace is using Git for version control (at least for developer templates) so it's conceivable they'll have a way to allow us to branch/version entire sites in the future and then switch between which version is live. This is just a guess, but it seems like the direction they'd go.
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